WHAT IF Check report

This file was created 2011-12-17 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb3p9s.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.513
CA-only RMS fit for the two chains : 0.268

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.558
CA-only RMS fit for the two chains : 0.312

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.545
CA-only RMS fit for the two chains : 0.319

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

All-atom RMS fit for the two chains : 0.470
CA-only RMS fit for the two chains : 0.182

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 0.477
CA-only RMS fit for the two chains : 0.193

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and D

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

2909 HDE   ( 761-)  A  -         Atom types
2910 HDE   ( 761-)  B  -         Atom types
2911 HDE   ( 761-)  C  -         Atom types
2912 HDE   ( 761-)  D  -         Atom types

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 642 OCS   ( 669-)  A
1327 VAL   ( 628-)  B
1368 OCS   ( 669-)  B
2094 OCS   ( 669-)  C
2306 ASP   ( 155-)  D
2820 OCS   ( 669-)  D

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:


Number of TLS groups mentione in PDB file header: 4

Crystal temperature (K) :100.000

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 7.87

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 251 ARG   ( 278-)  A
 286 ARG   ( 313-)  A
 342 ARG   ( 369-)  A
 395 ARG   ( 422-)  A
 509 ARG   ( 536-)  A
 609 ARG   ( 636-)  A
 810 ARG   ( 111-)  B
 864 ARG   ( 165-)  B
 882 ARG   ( 183-)  B
 959 ARG   ( 260-)  B
1076 ARG   ( 377-)  B
1170 ARG   ( 471-)  B
1208 ARG   ( 509-)  B
1220 ARG   ( 521-)  B
1486 ARG   (  61-)  C
1536 ARG   ( 111-)  C
1608 ARG   ( 183-)  C
1703 ARG   ( 278-)  C
1847 ARG   ( 422-)  C
1896 ARG   ( 471-)  C
1934 ARG   ( 509-)  C
1961 ARG   ( 536-)  C
1967 ARG   ( 542-)  C
2212 ARG   (  61-)  D
2262 ARG   ( 111-)  D
2334 ARG   ( 183-)  D
2418 ARG   ( 267-)  D
2429 ARG   ( 278-)  D
2622 ARG   ( 471-)  D
2687 ARG   ( 536-)  D
2763 ARG   ( 612-)  D
2853 ARG   ( 702-)  D

Warning: Tyrosine convention problem

The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0

 110 TYR   ( 137-)  A
 114 TYR   ( 141-)  A
 307 TYR   ( 334-)  A
 388 TYR   ( 415-)  A
 413 TYR   ( 440-)  A
 433 TYR   ( 460-)  A
 656 TYR   ( 683-)  A
 836 TYR   ( 137-)  B
 840 TYR   ( 141-)  B
1033 TYR   ( 334-)  B
1114 TYR   ( 415-)  B
1139 TYR   ( 440-)  B
1159 TYR   ( 460-)  B
1237 TYR   ( 538-)  B
1382 TYR   ( 683-)  B
1562 TYR   ( 137-)  C
1566 TYR   ( 141-)  C
1667 TYR   ( 242-)  C
1759 TYR   ( 334-)  C
1840 TYR   ( 415-)  C
1865 TYR   ( 440-)  C
1885 TYR   ( 460-)  C
2108 TYR   ( 683-)  C
2288 TYR   ( 137-)  D
2292 TYR   ( 141-)  D
2341 TYR   ( 190-)  D
2485 TYR   ( 334-)  D
2566 TYR   ( 415-)  D
2591 TYR   ( 440-)  D
2611 TYR   ( 460-)  D
2834 TYR   ( 683-)  D

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

 125 PHE   ( 152-)  A
 139 PHE   ( 166-)  A
 179 PHE   ( 206-)  A
 180 PHE   ( 207-)  A
 187 PHE   ( 214-)  A
 190 PHE   ( 217-)  A
 250 PHE   ( 277-)  A
 290 PHE   ( 317-)  A
 304 PHE   ( 331-)  A
 311 PHE   ( 338-)  A
 320 PHE   ( 347-)  A
 324 PHE   ( 351-)  A
 355 PHE   ( 382-)  A
 364 PHE   ( 391-)  A
 375 PHE   ( 402-)  A
 416 PHE   ( 443-)  A
 484 PHE   ( 511-)  A
 502 PHE   ( 529-)  A
 627 PHE   ( 654-)  A
 677 PHE   ( 704-)  A
 851 PHE   ( 152-)  B
 865 PHE   ( 166-)  B
 888 PHE   ( 189-)  B
 905 PHE   ( 206-)  B
 906 PHE   ( 207-)  B
And so on for a total of 82 lines.

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  43 ASP   (  70-)  A
  63 ASP   (  90-)  A
  64 ASP   (  91-)  A
  80 ASP   ( 107-)  A
  91 ASP   ( 118-)  A
 119 ASP   ( 146-)  A
 128 ASP   ( 155-)  A
 150 ASP   ( 177-)  A
 154 ASP   ( 181-)  A
 170 ASP   ( 197-)  A
 189 ASP   ( 216-)  A
 232 ASP   ( 259-)  A
 278 ASP   ( 305-)  A
 303 ASP   ( 330-)  A
 325 ASP   ( 352-)  A
 328 ASP   ( 355-)  A
 353 ASP   ( 380-)  A
 374 ASP   ( 401-)  A
 427 ASP   ( 454-)  A
 498 ASP   ( 525-)  A
 518 ASP   ( 545-)  A
 524 ASP   ( 551-)  A
 542 ASP   ( 569-)  A
 551 ASP   ( 578-)  A
 558 ASP   ( 585-)  A
And so on for a total of 137 lines.

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  36 GLU   (  63-)  A
  42 GLU   (  69-)  A
  79 GLU   ( 106-)  A
 166 GLU   ( 193-)  A
 221 GLU   ( 248-)  A
 279 GLU   ( 306-)  A
 300 GLU   ( 327-)  A
 306 GLU   ( 333-)  A
 308 GLU   ( 335-)  A
 319 GLU   ( 346-)  A
 335 GLU   ( 362-)  A
 360 GLU   ( 387-)  A
 403 GLU   ( 430-)  A
 434 GLU   ( 461-)  A
 445 GLU   ( 472-)  A
 456 GLU   ( 483-)  A
 476 GLU   ( 503-)  A
 492 GLU   ( 519-)  A
 514 GLU   ( 541-)  A
 538 GLU   ( 565-)  A
 612 GLU   ( 639-)  A
 693 GLU   ( 720-)  A
 731 GLU   (  32-)  B
 740 GLU   (  41-)  B
 762 GLU   (  63-)  B
And so on for a total of 95 lines.

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 393 ILE   ( 420-)  A      CA   CB    1.62    4.5
 856 ASN   ( 157-)  B      CB   CG    1.64    4.8
 902 THR   ( 203-)  B      CA   CB    1.63    4.9
1193 VAL   ( 494-)  B      CB   CG2   1.68    4.9
1496 VAL   (  71-)  C      CA   CB    1.61    4.1
2222 VAL   (  71-)  D      CA   CB    1.61    4.1
2273 ILE   ( 122-)  D      CG1  CD1   1.69    4.4
2571 ILE   ( 420-)  D      CA   CB    1.63    5.2
2590 PRO   ( 439-)  D      N    CA    1.53    4.0
2611 TYR   ( 460-)  D      CD2  CE2   1.50    4.1
2902 ILE   ( 751-)  D      CA   CB    1.61    4.2

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.993167  0.000051 -0.000278|
 |  0.000051  0.992140 -0.000131|
 | -0.000278 -0.000131  0.994147|
Proposed new scale matrix

 |  0.010763  0.000000  0.003755|
 |  0.000000  0.007568  0.000001|
 |  0.000002  0.000001  0.008675|
With corresponding cell

    A    =  92.924  B   = 132.127  C    = 122.103
    Alpha=  90.015  Beta= 109.249  Gamma=  89.999

The CRYST1 cell dimensions

    A    =  93.560  B   = 133.170  C    = 122.810
    Alpha=  90.000  Beta= 109.240  Gamma=  90.000

Variance: 4632.223
(Under-)estimated Z-score: 50.160

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

  45 ARG   (  72-)  A      CG   CD   NE  101.88   -5.1
  92 HIS   ( 119-)  A      CG   ND1  CE1 109.70    4.1
  94 ARG   ( 121-)  A      CG   CD   NE  103.15   -4.3
 224 HIS   ( 251-)  A      CG   ND1  CE1 109.71    4.1
 282 LYS   ( 309-)  A      CA   CB   CG  105.52   -4.3
 323 ASP   ( 350-)  A     -C    N    CA  114.47   -4.0
 350 ARG   ( 377-)  A      CG   CD   NE  101.77   -5.1
 422 HIS   ( 449-)  A      CG   ND1  CE1 109.69    4.1
 736 ARG   (  37-)  B      CG   CD   NE  118.66    4.8
 771 ARG   (  72-)  B      CG   CD   NE  102.45   -4.7
 820 ARG   ( 121-)  B      CG   CD   NE  102.85   -4.5
 834 HIS   ( 135-)  B      CG   ND1  CE1 110.24    4.6
1069 VAL   ( 370-)  B      N    CA   CB  101.53   -5.3
1076 ARG   ( 377-)  B      CG   CD   NE  103.03   -4.4
1094 HIS   ( 395-)  B      CG   ND1  CE1 109.61    4.0
1248 HIS   ( 549-)  B      CG   ND1  CE1 109.75    4.1
1251 LEU   ( 552-)  B      CA   CB   CG  131.21    4.3
1301 VAL   ( 602-)  B      C    CA   CB  102.31   -4.1
1438 HIS   ( 739-)  B      CG   ND1  CE1 109.79    4.2
1462 ARG   (  37-)  C      CB   CG   CD  103.36   -5.4
1584 ILE   ( 159-)  C      C    CA   CB  118.00    4.2
1584 ILE   ( 159-)  C      CA   CB   CG2 118.86    4.9
1584 ILE   ( 159-)  C      CB   CG1  CD1 104.33   -4.5
1608 ARG   ( 183-)  C      CG   CD   NE  119.12    5.1
1708 GLU   ( 283-)  C      C    CA   CB  101.51   -4.5
1854 HIS   ( 429-)  C      CG   ND1  CE1 109.83    4.2
2003 ASP   ( 578-)  C     -C    N    CA  110.60   -6.2
2150 ASP   ( 725-)  C      C    CA   CB   99.31   -5.7
2223 ARG   (  72-)  D      CG   CD   NE  102.94   -4.4
2270 HIS   ( 119-)  D      CG   ND1  CE1 109.75    4.2
2387 HIS   ( 236-)  D      CG   ND1  CE1 110.05    4.4
2426 HIS   ( 275-)  D      C    CA   CB  102.03   -4.2
2443 HIS   ( 292-)  D      CG   ND1  CE1 109.71    4.1
2491 LEU   ( 340-)  D      CB   CG   CD1 124.70    4.7
2528 ARG   ( 377-)  D      CG   CD   NE  103.32   -4.2
2543 HIS   ( 392-)  D      CG   ND1  CE1 110.08    4.5
2580 HIS   ( 429-)  D      CG   ND1  CE1 110.19    4.6
2600 HIS   ( 449-)  D      CG   ND1  CE1 110.09    4.5

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  36 GLU   (  63-)  A
  42 GLU   (  69-)  A
  43 ASP   (  70-)  A
  63 ASP   (  90-)  A
  64 ASP   (  91-)  A
  79 GLU   ( 106-)  A
  80 ASP   ( 107-)  A
  91 ASP   ( 118-)  A
 119 ASP   ( 146-)  A
 128 ASP   ( 155-)  A
 150 ASP   ( 177-)  A
 154 ASP   ( 181-)  A
 166 GLU   ( 193-)  A
 170 ASP   ( 197-)  A
 189 ASP   ( 216-)  A
 221 GLU   ( 248-)  A
 232 ASP   ( 259-)  A
 251 ARG   ( 278-)  A
 278 ASP   ( 305-)  A
 279 GLU   ( 306-)  A
 286 ARG   ( 313-)  A
 300 GLU   ( 327-)  A
 303 ASP   ( 330-)  A
 306 GLU   ( 333-)  A
 308 GLU   ( 335-)  A
And so on for a total of 264 lines.

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 348 LEU   ( 375-)  A      CG     8.3   -18.48   -33.01
1074 LEU   ( 375-)  B      CG     6.7   -21.30   -33.01
1539 ILE   ( 114-)  C      CB     6.3    40.53    32.31
1584 ILE   ( 159-)  C      CB    -7.8    22.18    32.31
2349 LEU   ( 198-)  D      CG     6.3   -22.00   -33.01
2526 LEU   ( 375-)  D      CG     6.4   -21.82   -33.01
2705 LEU   ( 554-)  D      CG     6.6   -21.33   -33.01
2784 LEU   ( 633-)  D      CG     6.2   -22.15   -33.01
The average deviation= 1.400

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 721 ILE   ( 748-)  A    4.75
2173 ILE   ( 748-)  C    4.58
1543 ASP   ( 118-)  C    4.23
2172 LYS   ( 747-)  C    4.15

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

1085 ASN   ( 386-)  B    4.94
 480 HIS   ( 507-)  A    4.80
2552 ASP   ( 401-)  D    4.57
2731 ASN   ( 580-)  D    4.52
 368 HIS   ( 395-)  A    4.42
1644 HIS   ( 219-)  C    4.27

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

2860 LYS   ( 709-)  D    -2.8
 903 PRO   ( 204-)  B    -2.8
1630 ILE   ( 205-)  C    -2.7
 422 HIS   ( 449-)  A    -2.6
 177 PRO   ( 204-)  A    -2.5
1802 ARG   ( 377-)  C    -2.5
1333 TYR   ( 634-)  B    -2.5
 399 PRO   ( 426-)  A    -2.5
 904 ILE   ( 205-)  B    -2.5
1148 HIS   ( 449-)  B    -2.5
2903 PRO   ( 752-)  D    -2.4
2356 ILE   ( 205-)  D    -2.4
   2 LEU   (  29-)  A    -2.4
1903 LYS   ( 478-)  C    -2.4
1629 PRO   ( 204-)  C    -2.4
2785 TYR   ( 634-)  D    -2.4
 857 LYS   ( 158-)  B    -2.4
2299 THR   ( 148-)  D    -2.3
 178 ILE   ( 205-)  A    -2.3
2009 LYS   ( 584-)  C    -2.3
 607 TYR   ( 634-)  A    -2.3
1874 HIS   ( 449-)  C    -2.3
2577 PRO   ( 426-)  D    -2.3
2059 TYR   ( 634-)  C    -2.3
2355 PRO   ( 204-)  D    -2.3
And so on for a total of 62 lines.

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  34 ARG   (  61-)  A  omega poor
  50 ASN   (  77-)  A  Poor phi/psi
  54 THR   (  81-)  A  omega poor
  70 ALA   (  97-)  A  omega poor
  72 SER   (  99-)  A  omega poor
 101 HIS   ( 128-)  A  Poor phi/psi
 135 VAL   ( 162-)  A  omega poor
 140 SER   ( 167-)  A  omega poor
 142 VAL   ( 169-)  A  omega poor
 150 ASP   ( 177-)  A  omega poor
 154 ASP   ( 181-)  A  omega poor
 197 GLU   ( 224-)  A  PRO omega poor
 202 ILE   ( 229-)  A  PRO omega poor
 208 ALA   ( 235-)  A  Poor phi/psi
 247 ALA   ( 274-)  A  Poor phi/psi
 251 ARG   ( 278-)  A  omega poor
 276 VAL   ( 303-)  A  omega poor
 311 PHE   ( 338-)  A  omega poor
 375 PHE   ( 402-)  A  omega poor
 419 ASP   ( 446-)  A  Poor phi/psi
 434 GLU   ( 461-)  A  PRO omega poor
 441 ASN   ( 468-)  A  Poor phi/psi
 442 TRP   ( 469-)  A  PRO omega poor
 452 ARG   ( 479-)  A  Poor phi/psi
 459 GLN   ( 486-)  A  Poor phi/psi
And so on for a total of 147 lines.

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

1669 SER   ( 244-)  C    0.36
1302 VAL   ( 603-)  B    0.36
1227 SER   ( 528-)  B    0.37
 613 VAL   ( 640-)  A    0.38

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   3 ALA   (  30-)  A      0
   8 SER   (  35-)  A      0
   9 HIS   (  36-)  A      0
  10 ARG   (  37-)  A      0
  13 ALA   (  40-)  A      0
  15 PRO   (  42-)  A      0
  18 PRO   (  45-)  A      0
  21 GLN   (  48-)  A      0
  33 THR   (  60-)  A      0
  34 ARG   (  61-)  A      0
  45 ARG   (  72-)  A      0
  48 SER   (  75-)  A      0
  49 GLU   (  76-)  A      0
  50 ASN   (  77-)  A      0
  57 GLN   (  84-)  A      0
  62 ALA   (  89-)  A      0
  64 ASP   (  91-)  A      0
  65 GLN   (  92-)  A      0
  69 ARG   (  96-)  A      0
  73 ARG   ( 100-)  A      0
  92 HIS   ( 119-)  A      0
  93 GLU   ( 120-)  A      0
  99 ILE   ( 126-)  A      0
 100 VAL   ( 127-)  A      0
 101 HIS   ( 128-)  A      0
And so on for a total of 1127 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

2225 GLY   (  74-)  D   2.06   58
  47 GLY   (  74-)  A   2.06   64
1499 GLY   (  74-)  C   2.06   58
 773 GLY   (  74-)  B   2.05   59

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

  11 PRO   (  38-)  A    0.13 LOW
  15 PRO   (  42-)  A    0.15 LOW
  22 PRO   (  49-)  A    0.15 LOW
  25 PRO   (  52-)  A    0.18 LOW
 113 PRO   ( 140-)  A    0.15 LOW
 220 PRO   ( 247-)  A    0.17 LOW
 352 PRO   ( 379-)  A    0.18 LOW
 405 PRO   ( 432-)  A    0.50 HIGH
 450 PRO   ( 477-)  A    0.48 HIGH
 548 PRO   ( 575-)  A    0.11 LOW
 631 PRO   ( 658-)  A    0.01 LOW
 751 PRO   (  52-)  B    0.15 LOW
 839 PRO   ( 140-)  B    0.08 LOW
 946 PRO   ( 247-)  B    0.12 LOW
 962 PRO   ( 263-)  B    0.12 LOW
1065 PRO   ( 366-)  B    0.11 LOW
1078 PRO   ( 379-)  B    0.09 LOW
1097 PRO   ( 398-)  B    0.52 HIGH
1236 PRO   ( 537-)  B    0.46 HIGH
1274 PRO   ( 575-)  B    0.06 LOW
1276 PRO   ( 577-)  B    0.15 LOW
1445 PRO   ( 746-)  B    0.11 LOW
1470 PRO   (  45-)  C    0.46 HIGH
1477 PRO   (  52-)  C    0.15 LOW
1791 PRO   ( 366-)  C    0.19 LOW
1804 PRO   ( 379-)  C    0.17 LOW
1818 PRO   ( 393-)  C    0.45 HIGH
1861 PRO   ( 436-)  C    0.18 LOW
1900 PRO   ( 475-)  C    0.16 LOW
1933 PRO   ( 508-)  C    0.47 HIGH
1962 PRO   ( 537-)  C    0.45 HIGH
2000 PRO   ( 575-)  C    0.06 LOW
2171 PRO   ( 746-)  C    0.15 LOW
2193 PRO   (  42-)  D    0.16 LOW
2200 PRO   (  49-)  D    0.16 LOW
2414 PRO   ( 263-)  D    0.15 LOW
2517 PRO   ( 366-)  D    0.10 LOW
2583 PRO   ( 432-)  D    0.49 HIGH
2625 PRO   ( 474-)  D    0.09 LOW

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 236 PRO   ( 263-)  A  -122.4 half-chair C-delta/C-gamma (-126 degrees)
 430 PRO   ( 457-)  A   117.1 half-chair C-beta/C-alpha (126 degrees)
 622 PRO   ( 649-)  A     7.4 envelop N (0 degrees)
 725 PRO   ( 752-)  A    45.1 half-chair C-delta/C-gamma (54 degrees)
 929 PRO   ( 230-)  B   -64.4 envelop C-beta (-72 degrees)
1014 PRO   ( 315-)  B  -113.5 envelop C-gamma (-108 degrees)
1131 PRO   ( 432-)  B   106.1 envelop C-beta (108 degrees)
1198 PRO   ( 499-)  B   123.4 half-chair C-beta/C-alpha (126 degrees)
1348 PRO   ( 649-)  B    -6.5 envelop N (0 degrees)
1548 PRO   ( 123-)  C   100.7 envelop C-beta (108 degrees)
1672 PRO   ( 247-)  C  -122.3 half-chair C-delta/C-gamma (-126 degrees)
1720 PRO   ( 295-)  C   -57.2 half-chair C-beta/C-alpha (-54 degrees)
1767 PRO   ( 342-)  C    47.3 half-chair C-delta/C-gamma (54 degrees)
1857 PRO   ( 432-)  C   104.1 envelop C-beta (108 degrees)
1882 PRO   ( 457-)  C   106.4 envelop C-beta (108 degrees)
2011 PRO   ( 586-)  C  -115.3 envelop C-gamma (-108 degrees)
2177 PRO   ( 752-)  C   -53.4 half-chair C-beta/C-alpha (-54 degrees)
2203 PRO   (  52-)  D    99.4 envelop C-beta (108 degrees)
2381 PRO   ( 230-)  D   -55.1 half-chair C-beta/C-alpha (-54 degrees)
2398 PRO   ( 247-)  D  -113.8 envelop C-gamma (-108 degrees)
2530 PRO   ( 379-)  D  -127.0 half-chair C-delta/C-gamma (-126 degrees)
2659 PRO   ( 508-)  D   102.0 envelop C-beta (108 degrees)
2726 PRO   ( 575-)  D  -129.3 half-chair C-delta/C-gamma (-126 degrees)
2745 PRO   ( 594-)  D  -119.1 half-chair C-delta/C-gamma (-126 degrees)
2903 PRO   ( 752-)  D   -26.4 half-chair C-alpha/N (-18 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 365 HIS   ( 392-)  A      ND1 <->  388 TYR   ( 415-)  A      CB     1.44    1.66  INTRA BL
2543 HIS   ( 392-)  D      ND1 <-> 2566 TYR   ( 415-)  D      CB     1.43    1.67  INTRA BL
1091 HIS   ( 392-)  B      ND1 <-> 1114 TYR   ( 415-)  B      CB     1.40    1.70  INTRA BL
1817 HIS   ( 392-)  C      ND1 <-> 1840 TYR   ( 415-)  C      CB     1.39    1.71  INTRA BL
2911 HDE   ( 761-)  C    B CBC <-> 2915 HOH   (3347 )  C      O      1.24    1.56  INTRA BL
2910 HDE   ( 761-)  B    B CBC <-> 2914 HOH   (3346 )  B      O      1.18    1.62  INTRA BL
2909 HDE   ( 761-)  A    B CBC <-> 2913 HOH   (3345 )  A      O      1.12    1.68  INTRA BL
1876 MET   ( 451-)  C      SD  <-> 2915 HOH   (3338 )  C      O      1.05    1.95  INTRA BL
2912 HDE   ( 761-)  D    B CBC <-> 2916 HOH   (3348 )  D      O      1.04    1.76  INTRA BL
2697 GLN   ( 546-)  D      CG  <-> 2916 HOH   (2742 )  D      O      0.97    1.83  INTRA
2639 ARG   ( 488-)  D      NE  <-> 2916 HOH   (2698 )  D      O      0.71    1.99  INTRA
2602 MET   ( 451-)  D      SD  <-> 2916 HOH   (3342 )  D      O      0.70    2.30  INTRA
 452 ARG   ( 479-)  A      NH2 <-> 2913 HOH   (2607 )  A      O      0.67    2.03  INTRA
1091 HIS   ( 392-)  B      CE1 <-> 1114 TYR   ( 415-)  B      CB     0.57    2.63  INTRA BL
2543 HIS   ( 392-)  D      CE1 <-> 2566 TYR   ( 415-)  D      CB     0.54    2.66  INTRA BL
2224 LYS   (  73-)  D      CD  <-> 2914 HOH   (2705 )  B      O      0.54    2.26  INTRA
 365 HIS   ( 392-)  A      CE1 <->  388 TYR   ( 415-)  A      CB     0.53    2.67  INTRA BL
1817 HIS   ( 392-)  C      CE1 <-> 1840 TYR   ( 415-)  C      CB     0.53    2.67  INTRA BL
1817 HIS   ( 392-)  C      ND1 <-> 1840 TYR   ( 415-)  C      CG     0.51    2.59  INTRA BL
 365 HIS   ( 392-)  A      CG  <->  388 TYR   ( 415-)  A      CB     0.51    2.69  INTRA BL
2543 HIS   ( 392-)  D      CG  <-> 2566 TYR   ( 415-)  D      CB     0.49    2.71  INTRA BL
 350 ARG   ( 377-)  A      NH1 <-> 2913 HOH   ( 995 )  A      O      0.48    2.22  INTRA BL
 365 HIS   ( 392-)  A      ND1 <->  388 TYR   ( 415-)  A      CG     0.48    2.62  INTRA BL
2914 HOH   (2197 )  B      O   <-> 2915 HOH   (3168 )  C      O      0.48    1.92  INTRA
1977 LEU   ( 552-)  C      CD1 <-> 1981 GLN   ( 556-)  C      NE2    0.47    2.63  INTRA
And so on for a total of 392 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 760 ARG   (  61-)  B      -6.88
1903 LYS   ( 478-)  C      -6.88
2630 ARG   ( 479-)  D      -6.82
 452 ARG   ( 479-)  A      -6.81
1178 ARG   ( 479-)  B      -6.81
 451 LYS   ( 478-)  A      -6.80
1904 ARG   ( 479-)  C      -6.75
  34 ARG   (  61-)  A      -6.64
1486 ARG   (  61-)  C      -6.61
1177 LYS   ( 478-)  B      -6.50
2272 ARG   ( 121-)  D      -6.46
 686 GLN   ( 713-)  A      -6.42
2864 GLN   ( 713-)  D      -6.41
1546 ARG   ( 121-)  C      -6.41
  94 ARG   ( 121-)  A      -6.40
2138 GLN   ( 713-)  C      -6.39
2629 LYS   ( 478-)  D      -6.36
 820 ARG   ( 121-)  B      -6.27
2648 ARG   ( 497-)  D      -6.21
1412 GLN   ( 713-)  B      -6.18
 470 ARG   ( 497-)  A      -6.12
1922 ARG   ( 497-)  C      -6.09
1196 ARG   ( 497-)  B      -6.07
 342 ARG   ( 369-)  A      -5.89
1457 GLU   (  32-)  C      -5.77
And so on for a total of 80 lines.

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: C

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: D

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

2731 ASN   ( 580-)  D   -2.59
1652 TRP   ( 227-)  C   -2.56
1407 ILE   ( 708-)  B   -2.51

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 318 ASP   ( 345-)  A     -  321 LYS   ( 348-)  A        -1.64
2227 GLU   (  76-)  D     - 2230 ALA   (  79-)  D        -1.67

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

2913 HOH   (1624 )  A      O     44.92   -9.18  -37.30
2913 HOH   (2153 )  A      O     43.44   -7.05  -38.99
2915 HOH   (2935 )  C      O    -12.47   -9.43   51.74

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

2913 HOH   (2784 )  A      O
2913 HOH   (3128 )  A      O
2914 HOH   (3189 )  B      O
2915 HOH   (2658 )  C      O
2916 HOH   (2804 )  D      O
ERROR. No convergence in HB2STD
Old,New value: 5303.330 5303.343

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

   9 HIS   (  36-)  A
  57 GLN   (  84-)  A
 459 GLN   ( 486-)  A
 488 GLN   ( 515-)  A
1067 GLN   ( 368-)  B
1158 ASN   ( 459-)  B
1328 HIS   ( 629-)  B
1491 ASN   (  66-)  C
1793 GLN   ( 368-)  C
1801 ASN   ( 376-)  C
1981 GLN   ( 556-)  C
1997 ASN   ( 572-)  C
2054 HIS   ( 629-)  C
2096 ASN   ( 671-)  C
2199 GLN   (  48-)  D
2519 GLN   ( 368-)  D
2610 ASN   ( 459-)  D
2697 GLN   ( 546-)  D
2780 HIS   ( 629-)  D
2822 ASN   ( 671-)  D

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

  14 GLU   (  41-)  A      N
  35 ASN   (  62-)  A      N
  50 ASN   (  77-)  A      N
  66 ASN   (  93-)  A      N
  98 ARG   ( 125-)  A      NE
 100 VAL   ( 127-)  A      N
 103 ARG   ( 130-)  A      NH2
 138 ARG   ( 165-)  A      NH1
 152 VAL   ( 179-)  A      N
 176 THR   ( 203-)  A      N
 180 PHE   ( 207-)  A      N
 181 ILE   ( 208-)  A      N
 189 ASP   ( 216-)  A      N
 200 TRP   ( 227-)  A      N
 202 ILE   ( 229-)  A      N
 208 ALA   ( 235-)  A      N
 225 ASN   ( 252-)  A      ND2
 240 ARG   ( 267-)  A      NE
 242 MET   ( 269-)  A      N
 324 PHE   ( 351-)  A      N
 359 ASN   ( 386-)  A      ND2
 365 HIS   ( 392-)  A      ND1
 367 GLY   ( 394-)  A      N
 370 VAL   ( 397-)  A      N
 376 THR   ( 403-)  A      N
And so on for a total of 189 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

  91 ASP   ( 118-)  A      OD2
 174 ASN   ( 201-)  A      OD1
 185 HIS   ( 212-)  A      ND1
 390 ASP   ( 417-)  A      OD2
 434 GLU   ( 461-)  A      OE2
 817 ASP   ( 118-)  B      OD2
 900 ASN   ( 201-)  B      OD1
 911 HIS   ( 212-)  B      ND1
1091 HIS   ( 392-)  B      ND1
1116 ASP   ( 417-)  B      OD2
1148 HIS   ( 449-)  B    A NE2
1160 GLU   ( 461-)  B      OE2
1543 ASP   ( 118-)  C      OD2
1626 ASN   ( 201-)  C      OD1
1637 HIS   ( 212-)  C      ND1
1817 HIS   ( 392-)  C      ND1
1842 ASP   ( 417-)  C      OD2
1874 HIS   ( 449-)  C    A NE2
1886 GLU   ( 461-)  C      OE2
1932 HIS   ( 507-)  C      ND1
2269 ASP   ( 118-)  D      OD2
2352 ASN   ( 201-)  D      OD1
2363 HIS   ( 212-)  D      ND1
2568 ASP   ( 417-)  D      OD2

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

2913 HOH   ( 871 )  A      O  0.96  K  4

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  14 GLU   (  41-)  A   H-bonding suggests Gln
  63 ASP   (  90-)  A   H-bonding suggests Asn; but Alt-Rotamer
 300 GLU   ( 327-)  A   H-bonding suggests Gln
 570 ASP   ( 597-)  A   H-bonding suggests Asn
 789 ASP   (  90-)  B   H-bonding suggests Asn; but Alt-Rotamer
 817 ASP   ( 118-)  B   H-bonding suggests Asn; but Alt-Rotamer
1026 GLU   ( 327-)  B   H-bonding suggests Gln
1224 ASP   ( 525-)  B   H-bonding suggests Asn
1342 ASP   ( 643-)  B   H-bonding suggests Asn
1515 ASP   (  90-)  C   H-bonding suggests Asn; but Alt-Rotamer
1543 ASP   ( 118-)  C   H-bonding suggests Asn
1752 GLU   ( 327-)  C   H-bonding suggests Gln
1955 GLU   ( 530-)  C   H-bonding suggests Gln
2102 ASP   ( 677-)  C   H-bonding suggests Asn; but Alt-Rotamer
2156 GLU   ( 731-)  C   H-bonding suggests Gln
2241 ASP   (  90-)  D   H-bonding suggests Asn; but Alt-Rotamer
2269 ASP   ( 118-)  D   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.848
  2nd generation packing quality :  -2.077
  Ramachandran plot appearance   :  -1.038
  chi-1/chi-2 rotamer normality  :  -1.277
  Backbone conformation          :  -0.395

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.007
  Bond angles                    :   0.920
  Omega angle restraints         :   1.207
  Side chain planarity           :   1.290
  Improper dihedral distribution :   1.146
  Inside/Outside distribution    :   1.068

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 1.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.4
  2nd generation packing quality :  -1.5
  Ramachandran plot appearance   :  -0.8
  chi-1/chi-2 rotamer normality  :  -0.6
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.007
  Bond angles                    :   0.920
  Omega angle restraints         :   1.207
  Side chain planarity           :   1.290
  Improper dihedral distribution :   1.146
  Inside/Outside distribution    :   1.068
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.